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Yorodumi- PDB-2p46: Complex of a camelid single-domain vhh antibody fragment with RNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p46 | ||||||
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Title | Complex of a camelid single-domain vhh antibody fragment with RNASE A at 2.5A resolution: se5b-ortho-2 crystal form with five se-met sites (L4M, M34, M51, F68M, M83) in vhh scaffold. | ||||||
Components |
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Keywords | HYDROLASE/IMMUNE SYSTEM / SEMET PHASING / CAMELID SINGLE-DOMAIN ANTIBODY / VHH / CAB-RN05 / RNASE A / YEAST SURFACE DISPLAY / HYDROLASE-IMMUNE SYSTEM COMPLEX | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Camelus dromedarius (Arabian camel) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Tereshko, V. / Uysal, S. / Koide, A. / Margalef, K. / Koide, S. / Kossiakoff, A.A. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold Authors: Tereshko, V. / Uysal, S. / Koide, A. / Margalef, K. / Koide, S. / Kossiakoff, A.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p46.cif.gz | 101.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p46.ent.gz | 84.1 KB | Display | PDB format |
PDBx/mmJSON format | 2p46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p46_validation.pdf.gz | 452.1 KB | Display | wwPDB validaton report |
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Full document | 2p46_full_validation.pdf.gz | 458.5 KB | Display | |
Data in XML | 2p46_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 2p46_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/2p46 ftp://data.pdbj.org/pub/pdb/validation_reports/p4/2p46 | HTTPS FTP |
-Related structure data
Related structure data | 2p42C 2p43C 2p44C 2p45C 2p47C 2p48C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 #2: Protein | Mass: 13341.001 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.5 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 8 Details: HAMPTON RESEARCH INDEX SCREEN, SOLUTION #93: ZN(CH2H3O2)2, PEG 3350, pH 8.0, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97911 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 1, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 15319 / Num. obs: 15319 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / SU B: 25.509 / SU ML: 0.267 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.791 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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